You don't want to use flush free, you'll need flush effect niacin, it's a different form which will be released quicker. Flush free won't be very effective which is probably why they've not made much progress, I'd swap that for flush effect niacin asap-
I was able to fully correct my ducklings deficiency by adding niacin capsules their water, but it did take time and I had to keep adding niacin to their water for a considerable amount of time. But ideally if you can get some, B complex would be far better.
Hydrotherapy is great, just ensure they're supervised (I'm sure you already know this, just making sure). It definitely does sound like a severe niacin deficiency, whether at this stage it can be fully reversed, I'm not sure, but it's definitely worth a shot
Are they able to stand at all? Able to walk at all? Can they paddle in the water?